Annota — AI-Powered Paper Annotation Assistant

Turn your PDF library into an intelligent research assistant.

AI reads your papers, highlights key findings, explains formulas, and writes structured notes — all saved back to your reference manager.

Features · Quick Start · Usage Examples · Screenshots · Roadmap

AI reads the paper → understands content → creates precise annotations

AI generates a structured reading summary with key findings, methods, and conclusions

git clone https://github.com/dengls24/annota.git
cd annota

python -m venv .venv

# Windows:
.venv\Scripts\activate
# macOS / Linux:
# source .venv/bin/activate

pip install pymupdf mcp

{
  "mcpServers": {
    "annota": {
      "command": "C:/path/to/annota/.venv/Scripts/python.exe",
      "args": ["C:/path/to/annota/annota/server.py"],
      "env": {
        "ZOTERO_DATA_DIR": "C:/Users/YourName/Zotero"
      }
    }
  }
}

{
  "mcpServers": {
    "annota": {
      "command": "/path/to/annota/.venv/bin/python",
      "args": ["/path/to/annota/annota/server.py"],
      "env": {
        "ZOTERO_DATA_DIR": "/Users/YourName/Zotero"
      }
    }
  }
}

# One command to read a full paper:
/annota-read "path/to/paper.pdf"

# Or natural language:
# Highlight the findings in this paper's abstract in green
"/Users/yourname/Zotero/storage/ABCD1234/paper.pdf"

/annota-read "path/to/paper.pdf"
/annota-annotate "path/to/paper.pdf"
/annota-summarize "path/to/paper.pdf"
/annota-review "path/to/paper.pdf" ISCA

# Make skills available in all projects
cp -r .claude/skills/ ~/.claude/skills/

把这篇论文摘要中的发现结果用绿色标出来
(Highlight the findings in this paper's abstract in green)
"E:\Zotero\storage\ABCD1234\Song et al. - 2025 - AI washing.pdf"

标注论文中的假设(H1, H2)，并用中文解释每个假设的理论基础
(Annotate the hypotheses (H1, H2) and explain the theoretical basis of each in Chinese)

解释论文中的核心公式，添加中文注释
(Explain the key formulas in this paper, add Chinese annotations)

标注结论部分的政策启示，添加中文总结笔记
(Highlight policy implications in the conclusion, add a Chinese summary note)

/annota-summarize "path/to/paper.pdf"

逐段阅读这篇论文，为每个重要段落添加中文批注
(Read this paper paragraph by paragraph, add Chinese annotations to each important section)

Phase 1 — Understand (lightweight)
  get_pdf_text_bulk(pdf, skip_refs=True)
  → Full text without coordinates
  → AI identifies which sentences to annotate

Phase 2 — Annotate (precise)
  get_pdf_layout_text(pdf, target_page_only)
  → Coordinates for 1–2 target pages
  batch_annotate(pdf, all_annotations)
  → Write everything in one call

annota/
├── annota/                        # MCP Server (Python)
│   ├── server.py                  # 9 tool registrations
│   ├── zotero_db.py               # SQLite read/write layer
│   ├── pdf_tools.py               # PyMuPDF text extraction
│   └── config.py                  # Constants & configuration
├── .claude/skills/                # Claude Code Skills
│   ├── annota-annotate/SKILL.md   # /annota-annotate
│   ├── annota-summarize/SKILL.md  # /annota-summarize
│   └── annota-review/SKILL.md     # /annota-review
├── docs/                          # Design documents
│   ├── annota-guide.md            # Usage guide (CN)
│   ├── large-pdf-design.md        # Large PDF handling design
│   ├── dev-notes.md               # Pitfalls & solutions
│   └── commercial-plan.md         # Commercialization plan
├── assets/                        # Screenshots
└── README.md